The visitors, who began the day in fourth place in Group C one point behind Northern Ireland, were frustrated until the 66th minute when Marko Pantelic accepted a welcome gift.
Northern Ireland's Steve Davis failed to look when he steered a pass-back to Lee Camp and Pantelic stole in to round the stranded keeper and finish into an empty net.
It was no more than Serbia deserved as Camp and some last-ditch defending had kept them at bay throughout with Aleksandar Kolarov and Milan Jovanovic being denied.
The Irish created few openings in the match although Chris Brunt did have a shot blocked shortly after half-time when the hosts briefly gained some forward momentum.
However, they were outplayed by the visitors despite Serbia having no support in the stadium after their fans were banned in the wake of violence in the abandoned match against Italy.
"I hope we have restored some faith in Serbian soccer after this win," Pantelic told reporters.
"We are confident that the fans will get behind us in our remaining three matches and hopefully we will win a play-off berth to give them something to cheer about."
Coach Vladimir Petrovic said his side got their just reward.
"Anxiety crept in after we failed to score in the first half but we desrved our win because we dominated the match.
"The group is wide open now and we have to stay focused to win our home match against the Faroe Islands on Tuesday."
Serbia are now level on 11 points with second-placed Slovenia, who lost 2-1 at home to Estonia and have played one game more.
Italy are the runaway group leaders with 19 points after grinding out a 1-0 victory in the Faroe Islands.
